What Effect We Have
by ds9jullian
Summary: John returns from another tour in Afghanistan only to find his best friend beaten and broken.  John must fight his own demons while trying to help Sherlock deal with the aftermath of something that should never have happened.
1. Chapter 1

Author's Note: I do now own Sherlock or any of the characters.

Dr. John Watson lay in his bunk trying to sleep but to no avail; it had been a very rough few days. His body and mind wouldn't and couldn't shut down; adrenalin still ran through his veins. Every time he closed his eyes he would only be woken by a noise from outside the small metal building or one of his roommates coming to bed. He just wanted to sleep but then even his sleep wasn't restful as the nightmares that had plagued him when he had returned to London had returned.

"John," called a quiet voice, he hadn't heard the door open but then his mind had been elsewhere.

"Mmm" he replied trying to appear asleep.

"Sir, have a phone call in the office." replied the voice.

"Can it wait, Mary?" asked John rolling over in his bunk.

"I don't' think so." she entered the small dark room. "I told the commander you were asleep, he asked me to wake you, it seems important."

"Who is it?"

"He wouldn't say."

John rolled himself out of his bunk and straightened his blood stained scrubs before heading out. He couldn't think of anything that would be important enough to drag him from his bunk at 3am after what had been a very long, difficult and frightening day. He quickly made his way across the compound, too lazy and tired to find a coat for the cold night air.

"Dr. Watson" said the commander as he entered the building that housed the command post. It was lit by only a few electric lights. "You have a phone call."

Even the commander looked very confused. No one got personal phone calls, and not in the middle of the night. The commander pointed to the phone that sat on a table in the corner of the room.

"John Watson" he said picking up the receiver.

"John," said a very familiar voice that explained just about everything.

"Mycroft." John replied.

"You have orders to be on the next transport home."

"Sherlock?"

"Yes,"

"I will see you in a couple of days."

John put the receiver down and turned to his commanding officer who was obviously reading a fax that had just come in on the secure line.

"Let me guess, I need to go pack." Said John.

"You have serious connections in the government." Replied the commander.

"I know." He paused. "But I wish I didn't."

John was not happy as he returned to his bunk, what was so damned important that Mycroft would drag him back from Afghanistan. He and Sherlock had not parted on the best of terms, and John had made it very clear that he never wanted to see or hear from the Holmes brothers every again. He wouldn't make a big deal out of it, he didn't have the energy right now and he really could do with a break from the tragedy of war. He hoped that this wasn't going to be one of the Holmes' brother little games.

The cargo plane landed at an air force base just outside of London, John grabbed his ruck sack and made his way off the air craft, and there in front of him was the black car. Mycroft stood leaning on the car dressed in his typical suit with his umbrella in hand. It had been two days since the phone call.

"Thank you for coming." Said Mycroft

"Like I was given any choice." Replied John.

"I am sorry to have to resort to such measures but I believe you will understand soon enough."

Nine months ago John had returned to Afghanistan after a rather large and dramatic falling out between himself and Sherlock Holmes. Mycroft had been witness to many of the events leading up to the blow up that had ended his time at 221B Baker Street. The car ride passed in silence between the two men. Athena was engrossed in her cell phone the whole time as normal. Mycroft was obviously distracted replying to all of his texts with very short answers and dismissing any phone calls that may have come in. John figured it might be because there was more going on than he believed.

After arriving at the family home Mycroft lead John down a long highly decorated hallway, and into a small room filled with computers monitors lining the walls. It looked like something out of a military command center showing views of every part of the house and grounds.

"John, I should warn you, what you are about to see is something that neither he nor I would want to share with anyone but I don't know what else to do."

Mycroft pressed a few buttons on a nearby key board and an image appeared on the main screen, it was of a small white room, with no decoration on the walls except for streaks of blood. A mattress lay in the corner, showing obvious damage, and a single individual sat huddled in the corner, it was Sherlock, although it was hard to tell.

"What happened?" asked John shocked by what he was seeing.

"He was attacked, kidnapped and held hostage for nearly three months."

"Moriarty?"

Mycroft nodded slightly.

"John, I have tried everything to help my brother." he paused. "You are my last hope to ever see my brother recover from this."

This explained why Mycroft had dragged him Afghanistan. If Mycroft believed that John was the only way to reach his brother then there was something very wrong.


	2. Chapter 2

In a nearby room that looked like a medical supply room John changed out of his army uniform and into some scrubs that Mycroft had given him. He also took a few moments to think before venturing in to see Sherlock for himself. The camera image had given him only a few clues as to his friend's condition. He knew that something was very wrong, and that Mycroft had brought him home for a very good reason. John would never be able to live with himself if he knew that something had happened to Sherlock and that he could have changed the outcome, and now he had that chance. We he was ready he stood outside the door to Sherlock's cell waiting, Mycroft had the key in his hand.

"Ready?" asked Mycroft.

John nodded; he was ready as he was ever going to be.

Mycroft unlocked the door with a metallic click.

"When you are done just knock, I will have someone standing by the door." he paused. "I have turned the camera off."

Mycroft pulled the door open and John stepped in. Sherlock still sat huddled in the corner, John approached slowly unable to predict Sherlock's reaction to his presence in the room. The first think John noticed about Sherlock was that he was thinner than ever, his face more angular although it was hard to tell, he hadn't shaved in many days and had was growing in a rather nice beard although it was a pale brown in contrast is his black curly mop of locks. What skinned that showed was cover with hundreds of cuts and scrapes in various stages of healing, many of them rather fresh. To see his friend like this hurt him a way that he had never felt before expect when the solider on his table was beyond help but unlike those time John knew that there was still time to save Sherlock.

"Sherlock" said John quietly trying not to scare his friend.

Sherlock looked up slowly.

"Go away." said Sherlock very off hand.

"No," he paused, "Your brother dragged me all the way from Afghanistan." replied John trying to be gentle.

"I don't need your help." said Sherlock

"I beg to differ."

"I don't want your help." yelled Sherlock.

"I am not asking."

"You're not real, John's dead." yelled Sherlock.

"Who told you that?" asked John suddenly aware it would be more difficult that he first thought to help Sherlock.

"Moriarty."

"oh." said John suddenly understanding.

John sat down next to Sherlock who was now shaking. Mycroft has not gone into any details about what had happened to his brother during his time with Moriarty but John now suspected that that time had caused Sherlock a great amount of physical and mental torment.

"I'm not going to hurt you." Said John as he reached out and took Sherlock's hand in his own.

Sherlock started to panic but after a few minutes he began to calm down. John didn't know what to say so he just sat there. There were so many questions he had but Sherlock wouldn't have any of the answers.

Mycroft sat in the video room; he had turned the camera back on worried that something had happened. John had gone into see Sherlock over an hour ago. What he saw when image appeared on the screen pulled at his heart, John sat on the floor of the room holding Sherlock in his arms, and Sherlock looked calmer than he had since the kidnapping. They both looked to be asleep. Seeing this Mycroft arranged for a meal to be delivered to them, John would surely eat and hopefully he could get Sherlock to eat something. He also arranged for a cart of medical supplied and kit to be put together if John managed to reach Sherlock. He only wanted the best for his brother and he would move heaven and earth to do it, which is just about what it had taken to get John home.

John was awake when the food was delivered; he only smiled at the assistant who placed the tray on the floor of the room by the door. The assistant didn't seem to be happy about having been given this duty but seeing that John was holding on to Sherlock helped to calm her nerves a little. John could guess that Sherlock had become violent, between her reaction and the blood on the walls. Sherlock started to stir when the door clicked shut and the lock slid back into place. The food would sit there untouched.

"John" said Sherlock quietly.

"Yes Sherlock, I'm still here." he replied.

Sherlock seemed lost and confused about his position, John watched as he looked around the room.

"John." repeated Sherlock.

"I'm not going anywhere."

Sherlock settled back to sleep in John's arm. John couldn't believe what he was seeing, the ever arrogant, self centered Sherlock Holmes was wrapped his arms beaten and broken.

An hour or so later John carefully lay Sherlock down on the mattress covering him with a thin blood stained blanket, he stood watching him for a few minutes making sure that Sherlock was still asleep. John was scared to leave Sherlock for too long. John went to the door and knocked gently. He needed to use the bathroom and get some supplies. He was met by one of my Mycroft's many assistants; John asked where the nearest bathroom was.

Sherlock was mercifully still asleep when he returned to the room not five minutes after leaving. John sat down on the floor, a cart of medical supplied within reach. He debated with himself if he should try to start tending to Sherlock and if so where should he begin. When moving Sherlock to the bed he discovered that his friend was covered with bed sores and infected wounds on top of the cuts and scrapes he had first seen when he walked in the door. He just sat watching Sherlock sleep, taking in the sight of his best friend trying to figure out what the hell had happened to him.

Six hours passed before Sherlock woke, according a conversation with Mycroft a few hours before over a cup of tea in the hallway outside the room, the door wide open for fear of Sherlock waking up alone, it was the most sleep Sherlock had managed in the two weeks since he had been found naked and hypothermic in Hyde Park. They agreed then that if his metal state was clam enough that John could take him up to a bedroom and get him cleaned up. John spent the time reading a newspaper, it was something to do but he couldn't read more than a dozen words before his mind would jump straight back Sherlock.

John turned when he heard the springs on the mattress creak, and he went back to Sherlock's side and took his hand.

"John" called Sherlock quietly.

"Yes, Sherlock, I am still here."

"John" called again, this time pulling himself up into a seating position and reaching out to embrace John again.

"I'm not going anywhere."

"Good." replied Sherlock.

Sherlock sat cuddling John for nearly an hour when John felt it was time to start pushing. Sherlock was thinner than John had ever seen him, badly dehydrated but it was hard to tell he was so pale to begin with. It was obvious he hadn't showered in over a week.

"Sherlock?"

"Hmm" replied Sherlock.

"Do you want something to eat?"

"No,"

"Will you let me look at you?"

Sherlock nodded, John could feel the motion of his head against his shoulder.

"Come on" said John pulling Sherlock to his feel. "Let's get you cleaned up."

Sherlock could hardly walk as they made their way across the room, the door opened but no one was present in the hallway when they entered. John slowly walked Sherlock to a bedroom suite upstairs. It was late; the moon was high on the horizon thought John as they passed a row of windows. Everything was already set up and ready to go when they reached the bedroom, John silently thank Mycroft for thinking ahead.

For the next hour Sherlock said nothing and did little more than move from when place to another when guided by John. This allowed John to give Sherlock a much needed bath, and then very carefully a shave before tending to his wounds. Tending to his wounds was a slow delicate process; Sherlock didn't say anything but John could read the pain on his face. He looked a lot better for the shave, more like the Sherlock he knew and cared for. John did the best he could to no hurt Sherlock as he cleaned and bandaged him, talking to him the whole time explain to him what he was doing so as to not frighten him. He was able to see that at some point Sherlock had been restrained; there was deep bruising on his wrists and ankles. There wasn't an inch of his body this didn't should evidence of injury. He got Sherlock into a clean pair of pajamas and got him to drink a small cup of tea and a piece of toast.

"John" said Sherlock, while John returned the plate and cup to the cart.

"Yes, Sherlock."

John turned around to see Sherlock sitting on the bed with his knees pulled up to his chest with his arm wrapped around him. He could see the distress in Sherlock's eyes.

"Come on, why don't you lay down." He paused. "I'm not going anywhere."

Sherlock lay down but stayed curled up until John sat down on the bed next to him, upon which Sherlock reached out and wrapped his arms around John. John didn't fight, he just let it happen, and praying that Sherlock would just fall asleep which he did very quickly.


	3. Chapter 3

Authors Note: This is just a little short chapter, I am sort of stuck at this point as to where to take the story, please share any ideas you might have.

John awoke to the sun light shining in the bedroom windows, it was morning. Sherlock still lay asleep next to him, he had rolled over sometime during the night allowing John to get his first reasonable night of sleep in sometime, although he could have done with more but it would have to do. John carefully crept off the bed for fear of waking Sherlock, and headed to the bathroom, Mother Nature was calling. He took a few minutes to tend to himself before returning to the bedroom, he wanted a shower but didn't want to risk it. John looked at the bed, the sheets were thrown on the floor and Sherlock was gone.

"Sherlock." called John what appeared to be an empty room.

John stood in the bathroom door quietly thinking what to do next, when he heard the quiet rush of labored breathing. The pitch was a dead give away to John. He slowly walked around to the far side of the bed. Sherlock was huddled in the small space between the wall and the bed, his whole body shaking. Although he couldn't see his face john was fairly sure that Sherlock had been crying. It was all the obvious signs of a panic attack; he was trying to pull off his bandages.

"Sherlock," said John kneeling down in front of him. "I was just in the bathroom."

John placed his hand on Sherlock's to stop him tearing at his bandages. After a few moments Sherlock looked up, John could see fear in those beautiful grey eyes that had once burned brightly.

"John."

"Yes, Sherlock, I'm here, you have nothing to fear."

John pulled Sherlock to his feet and sat him back down on the bed. John sat down and wrapped his arm around his friend and pulling him close as to calm him as he continued to shake.

"Why don't we try finding some tea and toast and then maybe watch some telly." Asked John once Sherlock was sitting peacefully next to him.

John sat reading while Sherlock slept next to him on the bed. That morning Sherlock had managed drink some tea and toast before a short walk around the house. After they tried to watch some telly but Sherlock nearly jumped out of his skin and half way across the room when the sound of a single gunshot rang out during a commercial. It had taken nearly an hour to talk Sherlock out from behind the sofa; this little episode had only made John sure that Sherlock had a serious case of PTSD. After a short visit with Mycroft during which Sherlock tried to hide behind John while never letting go of his iron grip on John's hand, John grabbed some lunch for himself before returning to the bedroom with Sherlock who was worn out from his earlier outburst John was reading the police report and investigation in to Sherlock's disappearance which Mycroft had kindly given to him. John could tell the difference between the work of Scotland Yard and that of Mycroft's people. What he read was rather disturbing, but the evidence photos from the hospital tore his heart to shreds. John found himself looking at the photos and then to figure that lay next to him, asking himself only one thing; what the hell had happened? He agreed with the report that he had been tortured, restrained, drugged and beaten, that was all very obvious by the physical injuries but at this point John was worried about his mental wellbeing. As far as John could tell, at the moment he was the only one that Sherlock didn't try to hind from actually right now all Sherlock wanted was to be with John.


	4. Chapter 4

**Authors Note: **This is actually the second version of the story. One of my reviews suggested that I need to add more emotion to the situation so here we go.

_Sherlock lay naked in a small dark concrete room, it was windowless and no larger than the bathroom at the Baker Street flat. He had long ago memorized every centimeter of the room by touch. He shivered against eh draft that flowed from the heavy metal door at his feet and the aching cold of the uncovered floor upon which he lay. He didn't move from the spot where his captors had dumped him sometime before, there was nowhere to go and it would be a water of precious energy. The silence brought only pain; it hurt him to the core of his battered and broken body. He had thoughts of death, because death would mean an end to the pain, he no longer had a reason to live. John was gone, he had watched the footage for hours and hours, having watched his death over and over and over and over. Each time the vehicle he was traveling in approached the rock outcropping his heart would leap from his chest as it was blow into a million pieces by and IED. He had seen it so many times every time he closed his eyes it would play in his mind. Every inch of his body of his body wretched with the pain of John's death. The torture was nothing compared to the pain he felt for losing the one person he had allowed into his heart. He had long since lost count of the days, now he only waited for the end to come. The game was over and John was gone. _

_The sound of the lock broke Sherlock from his trance; he lay perfectly still knowing what was to come just as it had so many times before. The heave door opened quickly straining the hinges, bright light streamed in blinding him even though closed eyes. Two large men grabbed him and pulled him from his cell. He didn't struggle that would only make things worse. He was dragged into the room down the hall, and strapped to the chair again._

Sherlock was violently shaking next to John, every inch of him struggling against invisible restraints.

"Sherlock," said John. "Sherlock."

He was trying to wake his friend from his nightmare. John couldn't grab him because it would only make it worse; he had learned that the first night while they were in the white room. Those had been some very scary hours. John had feared for Sherlock's life.

After a moment Sherlock's eyes flashed open and his body went limp.

"John." He called in a panic.

"Sherlock, I'm right here." Replied John taking Sherlock's hand in his own.

"John." He called again much more calmly.

"It was a nightmare, you are safe." Said John.

John rubbed small circles on the back of Sherlock's hand with his thumb trying to calm him.

"Do you want to talk about it?" asked John when Sherlock's heart beat and respiration had slowed considerably.

"I was in the closet where they kept me, it was dark and cold." Sherlock's voice waivered and he spoke and his body began to curl up on itself. "The door opened and light blinded me as I was . . . "

Sherlock couldn't finish, his body began to shake and tears began to stream down his face.

John reached out and pulled the thin man into his arms

"You're safe now; no one is going to hurt you." Said John as he rubbed small circles on Sherlock's back to calm him again.

Sherlock used what little strength he had left to draw himself closer to John, tucking his head into John's shoulder and held on to him as an anchor and a reminder that John was very real and very much alive. John took long slow breaths trying to control his emotions, to see Sherlock like this hurt him in a way he had never known before. Even with all he had seen in war this hurt like nothing before it.

XXXXXX

Mycroft knocked gently on the bedroom door, it was nearly noon and he hadn't seen either John or Sherlock since midday yesterday. When he didn't get an answer he placed his hand on the door knob and slowly opened the door. Sun light filled the large bed room; Mycroft found John once again holding his little brother is a strong comforting embrace when he entered the bedroom that had become their home in the last few days. Sherlock was wearing one of John's jumpers, and his head was resting on John's shoulder, and appeared to be asleep.

"How is he?" asked Mycroft quietly approaching the bed.

John had heard the knock at the door but had not replied for fear of waking Sherlock. Mycroft's appearance wasn't a surprise, it was just a matter of time before he would come looking for an update on his brother.

"Asleep for now," said John slowly easing Sherlock on to the mattress. "He doesn't sleep for an hour or so before a nightmare wakes him."

"He keeps reliving moments from his captivity." Added John after a few moments.

John and Mycroft watched as Sherlock stirred but didn't wake. John pulled a blanket over Sherlock.

"Can I get you anything?" asked Mycroft maintaining his stoic demeanor.

"Tea." said John

"I will have the kitchen bring you some lunch."

"Thank you." said John moving to a nearby chair, he was tired and sore from holding Sherlock for so long..

"If you need anything, just ask." said Mycroft.

Mycroft went on his way, closing the door behind him, leaving John to tend to Sherlock.


	5. Chapter 5

Author's Note: I am not very happy with how this section of the story turned out. I rewrote the last chapter already and reposted it. I will probably end up rewriting this one sometime in the near future.

John walked down the long hallway to Mycroft's office having done something that he wasn't happy about but it was something that both he and Sherlock needed. John had sedated Sherlock, neither of them had slept properly in days and John couldn't leave Sherlock for more than a couple of minutes at time, it was wearing on him. Sherlock was sleeping soundly under the supervision of a nurse, John wouldn't leave him unattended. He was to visit with Mycroft for a few minutes and then he would shower and turn in for some seriously needed sleep.

The door to Mycroft's office was open when he arrived, so he figured it was a sign that he could enter.

"Ah, John." said Mycroft. "How is he?"

"Asleep, as he should be for the next twelve hours."

"So you did it?" asked Mycroft.

"Yes," replied John.

Mycroft pushed some files in to a drawer, got up from his chair and walked around his desk. He sat down in the chair next to John.

"John, I know that you and my brother did not part on the best of terms and that you felt that returning to Afghanistan was the only way you could make a clean break." Mycroft paused. "May I ask you what your fight was about?"

"Milk,"John paused. "The bloody milk, again."

"That's it?" asked Mycroft.

"Yes and no, it started with the milk and then it just exploded. I wanted a cup of tea after a shift at the clinic, I went to get milk from the fridge and the pint that I had purchased the day before was gone. I got mad at him; it hadn't been an easy day. Sherlock said some very mean things in rebuttal, that I shouldn't have taken the way I did. I don't think he understood what he was doing, he was just being Sherlock." John paused. "But I was so mad at him. I couldn't listen him say those things. It was the last straw."

Mycroft didn't say anything; he just sat watching John, doing his thing just like Sherlock. John was telling the truth but there was something more to the story that he wasn't tell. Mycroft didn't know if it was worth pushing the issue or not.

"I went to stay with Harry for a few days before I got lucky and they shipped me out."

There was a more silence, John began to grown uncomfortable.

"John, you are the first person in a very, very long time that my brother has let in." Mycroft paused for a moment. "You gave him something that he had never had before, someone to be there for him. I am shocked you lasted as long as you did and I honestly believe you at the first to truly gain Sherlock's trust. When you left I knew it would change him but I guess we will never know."

Mycroft poured himself a drink, and then poured one for John and handed it to him.

"What happened after I shipped out?" asked John taking the glass from Mycroft.

"Well, for about the first week or so he seemed okay enough, nothing out of ordinary except that I got a call from DI Lestrade asking where you were when he showed up at a crime scene without you and when asked he avoided the question. Late in the second week, he got into a fight with Anderson at a crime scene after he had been making jokes about you leaving Sherlock."

"Damn that man, he doesn't know when to bloody well shut up." replied John, he had seen the two of them.

"Lestrade let the matter drop, and then the downward spiral began, after solving the murder of the little boy he returned to Baker Street and holed himself up in the flat. Even a good murder couldn't get him out of the flat, after about ten days I finally went to see him after Mrs. Hudson called with her concerns and he was nowhere to be found. What I did find was evidence that suggests he may have been using again but it was only a couple of needles and morphine which he stole from you by number on the bottle."

John had to process this information.

"That explains the missing vial when I came to get my things." added John.

"I checked the CCTV footage and it showed him being taken from the flat during the night two days prior by a group of men dressed in black in an unmarked cab." Mycroft paused. "There was nothing in the way of clues or notes, he was just gone. I did everything I could to find him but nothing could be found. I used every contact, called in many personal favors searching for him but there was nothing there."

Mycroft stood and began to pace the office.

"Then two months to the day, he was found by a copper in Hyde Park behind a skip at about two in the morning. Naked, and wrapped in only a blanket. Lestrade called me immediately, he was taken to A&E where they did what they could and then I had him transferred here." He paused. "The rest you've seen."

John had read the medical file more times than he could count, and watched hours and hours of footage from before he had arrived.

"Yes," replied John calmly flexing his hands as he looked at the floor.

"I have a meeting with MOD in ten minutes so why don't you go get some rest?" said Mycroft. "We can continue this at a later time."

John silently stood and left Mycroft's office, he made his way down the long hallway back to his charge. He would check on Sherlock before showering and getting some sleep for himself.


	6. Chapter 6

Author's Note: This is all I have for the moment, I am having a serious case of writer's block.

John stood in the shower thinking, he always did his best thinking there. There were minimal interruptions and little to distract you from where you were going with your thoughts. John couldn't work out what was going on in Sherlock's mind. Sherlock's mind had always been a huge mystery to him but now when John most needed to know what was going in there Sherlock was giving him fewer clues. In the days since his return John had noticed many things. Sherlock couldn't and wouldn't be left alone. Sherlock did not like to be in the presence of anyone other than John, except for Mycroft who he would tolerate if only accompanied by John, everyone else would cause him to begin panicking. Sherlock was scared of the shower, something about the running way freaked him out. In all the time John had lived with Sherlock he had never once known him to take a bath and John had given him five. If they ate in the dining room John would have to drag a chair in from the kitchen, Sherlock wouldn't sit in any of the dining room chairs. John figured it had something to do with the arms on the fancy dining room chairs. He tried to think of what he could do to help Sherlock get over these but he could only do that if he knew the why but Sherlock wasn't ready to share yet. John was too exhausted to think much more so before he fell asleep on his feet he retired to the bed, choosing to stay with Sherlock by sleeping next to him.

XXX

Mycroft once again knocked softly on the bedroom door, when there was no answer he slowly opened the door. Asleep on the bed were John and Sherlock, hands entwined in the middle of the bed, their bodies facing each other in their sleep. Mycroft hated to wake John but the phone call that he had just received was news that John wanted to hear. It had been a good six hours since he had left Mycroft's office so he should be slightly more functional that before. Mycroft was forgiven the burden of waking John, as he stirred as Mycroft crossed the room. Obviously his military training still guided him. Mycroft waited for John to pull himself into a sitting position. John did not let go of Sherlock's hand as he sat himself up in the large bed.

"Lestrade just called, they have found where Sherlock was kept captive." Said Mycroft after giving John a few moments to get oriented.

The look on John's face told him everything he needed to know. John was torn between getting his questions answered and leaving Sherlock.


	7. Chapter 7

Author's Note: Thank You for being so patient, I have an idea of where I want to take the story but finding the time to actually write it is another matter all together. Please take the time to review it motivates me to write more.

What Effect We Have Chapter 7

John got out of the car that Mycroft had provided him with. There were a half dozen official vehicles parked around an old warehouse, an officer standing along the perimeter lifted the tape to allow to John in. There were no questions, everyone knew of Sherlock's attack. Donavan was standing outside the warehouse waiting for John; Lestrade was still inside with the forensics team.

"John." Said Donavan as he approached. "Everyone is inside."

John signaled for her to lead the way, he was physically and mentally exhausted but he knew that he had to see this. It would be the only way to understand what Sherlock had been though and only then could the healing process begin. He followed Sally in a pair of rusting metal doors, down a short hall, and then down a set of dark stairs to the basement of the warehouse.

"A couple of teens called it in, they were looking for a place to party when they found it." she paused. "I warn you, it isn't pleasant in there."

A group of forensic specialists dressed in blue jumpsuits wandered in and out of the dusty air illuminated by work lights they had brought in. When they saw John they stepped out of the way to allow him in. John did not hesitate as he entered the room but the moment he took the room in his stomach turned over.

Lestrade stood in the light of the window small window. He said nothing wanting to give John some time to process the scene. In the center of the room sat a high back heavy wooden chair bolted to the floor, with leather straps to restrain the person who was placed there, covered in stains that appeared to be more than just blood. The straps showed evidence of having been fought against; the width was the same as the bruises on Sherlock's wrists and ankles. Chains hung from the ceiling in the darkest corner of the room. A garden hose with a sprayer sat coiled in another corner water still dripping from the connection. He covered his mouth with his hand; the smell was putrid, like death and rotting flesh. Dark stains covered the floors and the walls, probably blood. Whoever had spent time in this room had suffered greatly at the hands of his captors. Everything he looked at tore at his heart.

"I called Mycroft because I knew you would want to see this."

"It explains a great deal." John paused. "The shower," he said pointing to the hose in the corner of the room. "Dining chairs with arms," he said indicating the chair in the center of the room.

"How is he doing?" asked Lestrade.

"Sedated," replied John.

"That bad." added Lestrade

John simply nodded.

"This is where he was tortured for information." said Lestrade pointed to a plastic bin by the entrance to the room."

John looked in to the bin, it was evidence, he could make out a cattle prod stained with blood, a leather whip, a piece of cane, a number of used needles, and a couple of vials of a commercially available drugs. The tools of torture, they matched Sherlock's injuries.

"We found another room down the hall that we believe was the room in which he was held when he was not here."

Lestrade started for the door, John followed him. They went nearly 100 meters down the hall to another room. A solid metal door with a heavy locking mechanism, reminiscent of a bunker.

"This building was used to make bombs during the war." said Lestrade answering John's unasked question.

Lestrade stepped to one side to allow John to enter this room alone. It was tiny maybe 3 meters by 3 meters, which explained his fear of confined spaces. This room was in no better shape, the same stained floor and walls, the same smell and it lacked windows meaning that once the door closed it was as dark as night.

"John, you okay in there?" asked Lestrade.

This broke John's trance, he was lost in his own thoughts. Years of service in the army and time on the fronts lines meant that he didn't have to use to much imagination to figure out what Sherlock's captors had done to him.

"Yes, sorry. I was just thinking." replied John.

John came out of room, the forensic team continued to work but they appeared to be almost done. John didn't imagine there was much life to find beyond that he tools of torture that they had already discovered. Hopefully Mycroft would be able to help Lestrade piece together the evidence to make an arrest in Sherlock's capture.

"I know how you feel, when I saw it I just couldn't help but imagine Sherlock strapped to that chair." Said Lestrade.

"John, why don't you head home and help Sherlock, I will call when I have more information."

John nodded, and turned to head out of the warehouse, he needed to breathe fresh air free of scent that didn't bombard his senses of the horrible scenes both past and present.

"Carson, would you walk Dr. Watson out please," said Lestrade.

XXXXXXXXXX

John sat in the back of the car as the driver drove him back to the Holmes Estate. What he had seen explained so much and it scared him, but it also gave him some much needed information to help Sherlock recover. It would take months if not years to help him and John knew that even then he may never be the person he once was. There was a long road ahead; John didn't know if he had it in him to go down that road.


	8. Chapter 8

Author's Note: I am working away slowly at this. I have a view more things to do before I can write the next few chapters, please be patient.

The car pulled in to the Holmes Estate just as the sun was beginning to rise in the east. Hopefully the kitchen would have a hot cup of tea and some toast waiting for him. The morning's weather reflected how John felt, gloomy and over cast. In the short time he had been at the crime scene he had learned enough to begin the process of helping Sherlock but there was one thing that still remained a mystery to him, how had they convinced Sherlock that he, John Watson was dead. John slowly made his way into the house, he had grown familiar with the estate in recent days so he started towards the kitchen in the hopes of find food and caffeine.

"Dr. Watson, is that you?" came a gentle female voice, belonging to one of the nurses that had come to help watch over Sherlock in the last few days.

"Yes," he replied dreading what was coming next. His first thought turned to Sherlock waking up without him being there.

"I thought you would like to know that Mr. Holmes is still asleep."

"Thank you." Said John relieved that it was nothing more than an update on his condition.

John had made sure before he left that Sherlock would never know that he had left, and if he had done his maths correctly he still had a good hour before Sherlock would begin to stir. In the kitchen he found a place set for him at the kitchen table, including a plate of eggs and toast, and a cup of tea. John was once again grateful for Mycroft Holmes ability to predict his needs so accurately. He sat down and began to slowly eat the still hot meal.

John returned to the rooms he now shared with Sherlock after his quiet meal in the house kitchen, it had been twenty minutes of personal heaven. Now it was time to begin the daily battles that were life with Sherlock. John found a new copy of the British Medical Journal and took his station in the arm chair next to the bed, Sherlock was just beginning to stir. A few pages in Sherlock began to shake, and toss. John quickly reached out and took Sherlock's hand in his, this calmed him.

"Sherlock, Lestrade and his team believe that they have found where you were held." Said John to his friend as they sat in the garden courtyard enjoying the beautiful afternoon.

John knew that he had to start getting Sherlock to talk about what had happened it him, all his previous attempts had been unsuccessful but now John had information if about what might have happened to him based on the evidence found at the warehouse.

Sherlock just continued to sit quietly watching a pair of nesting birds in a nearby tree.

"While you were asleep early this morning I went and saw it." Continued John.

"What did you see?" asked Sherlock.

His voice made it clear that he was just being courteous, and that he really didn't want to discuss it. John didn't really want to push the subject but he also knew that if he didn't he was just prolonging the inevitable.

"In the basement of a warehouse there were two rooms separated by a length of hallway, they were cold dark concrete rooms; one no larger than a bathroom the other significantly larger." He paused. "You were held in the smaller room between your visits to the larger room where your captures did unspeakable things to you."

John used his military and medical training to keep his wits about him as he talked about this difficult subject, he wasn't ready to go into detail yet.

"What do you know about what they did to me?" said Sherlock fighting to keep in control.

Sherlock's level of self control had been one of the skills that had fallen victim to his time in the cell, it was very understandable, he had been put in such a position where he had no control at all.

"I know that you were tortured from the injuries that you suffered and that they match the evidence found in the warehouse." Said John calmly.

Sherlock was now standing at the edge of the courtyard looking out across the garden before him.

"You don't have any idea what they took from me" replied Sherlock rapidly growing angry.

John knew he had to move carefully, if he wasn't careful this could blow up in his face.

"They took everything that made me who I was." He paused. "I am no longer that person, I have no control, my mind is blank, I am as useless as those who did this to me."

Sherlock was growing very aggravated and angry as he paced the courtyard only a few meters from John. He was rapidly losing any self control that he did have.

"There is nothing left except the burning pain."

John was thrown off. Pain, there was nothing in Sherlock's medical records to show that he should be suffering from severe physical pain. Many of his wounds had healed, only the yellow shadows of bruises remained on his pale skin.

Sherlock's hands began is shake, he quickly grabbed one with the other, hoping that John did not notice, but the shaking continued to spread. John quickly got up from where he sat and approached Sherlock who fought to keep control.

John reached him in time to gently lower him to the ground before he is legs gave out from under him. John pulled him close and held him as his body continued to shake as Sherlock's body contracted in pain.


	9. Chapter 9

Author's Note: Sorry this took so long, I have been very busy with work. I am still working on how to end this story, ideas?

John sat next to a now sleeping Sherlock; his fit in the garden had passed quickly but had left Sherlock exhausted. Mycroft had tried to help but Sherlock had become rather agitated so John alone had helped Sherlock back to their room for him to rest. John wanted to know if it had been a physical event or if it had been from remembering the events during his time at the hands of his torturer but it would have to wait there was no way that Sherlock would go near a hospital, every time someone mentioned the word he would get upset. John suspected that it had something to do with how he had been tortured. John was thinking long and hard about Sherlock's mention of a burning pain within. Was the pain physical or was it mental, John had already looked over Sherlock's medical records there was nothing to indicate that he should still be in pain. Sherlock was opposed to pain killers, especially anything more powerful than what you would find at your corner pharmacy. John had already decided to check Sherlock over during his next bath, wanted to know if he had missed something important. All John could do for now was to wait for Sherlock to wake it was just a matter of time before his sleep would be disturbed by another nightmare.

A few hours and several cups of tea later the inevitable happened, the nightmares returned.

"Sherlock" said John trying to wake Sherlock from his nightmare. "Sherlock" he repeated louder.

Sherlock's eyes opened wide.

"I'm right here Sherlock." Said John trying to focus his friend's attention and bring him back to the reality that he was safe and sound.

Sherlock reached out seeking the comfort of his friend, John instinctively pulled Sherlock closer. Sherlock's need for personal contact had grown significantly since John's return. John held Sherlock running his hands up and down the detectives back hoping to calm him and possibly solve the mystery of why he was in pain.

"Sherlock," he said softly still holding his friend. "You said you had a burning pain, I need you to tell me where it hurts."

Sherlock remained motionless for some time. Then Sherlock began to move slowly, first backing away from his embrace, he placed his hand on John's shoulder and slowly slid it down his arm, and taking John's hand by the wrist. He guided John's hand to his left side just below his ribs.

"There." He said softly.

John used his fingers to gently examine the area though it was hard to feel much through the material of Sherlock's shirt. Something just didn't feel right.

"Can I have a closer look." Asked John.

He helped Sherlock to lay back down, John gently pulled up Sherlock's shirt. He had seen the 12 cm long scar many times and thought nothing of it but now he began to wonder. It looked like it had been tended to properly, John had assumed that it had been a doctor caring for Sherlock before John had returned but now that was in question. He could feel something but he didn't know what.

"Sherlock, I need to see what they did to you. We can do this a couple of different ways, we can go to the hospital have a look at what's in there and then have it removed, or . . . " John paused to read Sherlock's reaction, and it was immediate.

"No hospitals, John."

"Will you let me do it?"

Sherlock nodded. Sherlock showed so much trust in John.

Several hours later John had everything he needed ready to go, Mycroft would do anything to help in the recovery of his brother. Sherlock still lay on the bed from where John had looked at him earlier, he hadn't said a word or moved an inch since their conversation. John gave Sherlock a sedative before having a nurse join them in the room. He used a local to numb the area before carefully preparing the area. He carefully cut into the scar tissue; John went slowly not wanted to do more damage than was absolutely necessary. He quickly found want he was looking for, he had seen something similar in his short time working in the surgery with Sarah, it was a sub dermal drug implant but he had never seen one so large. John quickly removed it, saving it for analysis my Mycroft's people. He cleaned the area before closing the wound again taking special care of the wound so that it wouldn't scare badly. He made sure to remove all the equipment before Sherlock woke up. Everything he did was to keep Sherlock calm, he was still so timid. John didn't want to start pushing to hard until all his physical injuries had healed.

Sherlock was still asleep, with John at his side when the results of the analysis the drug came in. No wonder Sherlock had been in pain, it was a drug of torture at that level of concentration and because of the nature of the drug it didn't show up in a standard drug screen. The fact that Sherlock had been able to function with the drugs in his system showed just how strong he still was. John was just happy to have it out of his system, and planned on taking a blood sample tomorrow to make sure it was the only one.

The sedative wore off slowly, John woke him before he could be plagued by another nightmare. Sherlock ate a sandwich and had a cup of tea without argument. John took this as a sign that Sherlock was feeling better.

"Sherlock, I can see you are feeling better." Said John sitting down next to Sherlock at the small table that had been set up in there room. "Well, I though you would want to know that your captures had given you a sub dermal drug implant containing several drugs used for torture." He paused. "Sherlock you have done amazing, given the drugs in your system you should have been screaming in agony for the last month. You are stronger than you know and we will get through this."


	10. Chapter 10

Author's Note: Finally, I have managed to spend some time working on this. I hope you all enjoy it.

John awoke to a wash of sun light across the room, he was stunned. Sherlock was still asleep next to him; they had gone a whole night without a nightmare or a panic attack. This was progress, real progress. He didn't move for fear of waking Sherlock from the first real sleep he had probably had since John had left him so many months ago. John stayed holding Sherlock's hand trying to figure out what to do next. He had already planned on a bath before a walk in the garden but maybe he should push a little harder today. He wanted to go back to Baker Street, he could go alone but he wanted to go with Sherlock but he didn't know if Sherlock was ready yet. London was always a buzz of people and John had yet to see any signs that Sherlock was ready to be around people again. It was probably too soon; maybe they needed to focus on more reasonable goals. Lestrade, he could call and ask him to come up. It would expose Sherlock to someone that he was reasonablely comfortable and get him use to being with people again. He knew he could do it Mycroft could do anything if you knew how to ask.

Sherlock didn't fuss while John helped him bath, maybe it was the drugs and his new level of cooperation was the result of them finally being out of his system. And much to John's surprise he cleared both the eggs and toast from his plate without complaint or prompting from John. Well, that was a leap and a bound in one morning. Maybe today wasn't the day to push Sherlock, he seemed to making enough strides on his own today but John had to wonder if it was real or if it was forced. He would leave the topic alone for now, off to the garden they went.

"I'm bored." Said Sherlock in a very familiar tone.

"What would you like to do?" replied John looking up from the paper.

"Go back to work."

"Sherlock, you are exhausted from walking from one end of the garden to the other. You're not ready."

Sherlock didn't like what John had just said, but he couldn't come up with an argument.

"Would you like to go visit Baker Street?" he paused. "Pick up some books, what about your violin?"

John was scared of how Sherlock would react.

"Brilliant." He said in that cheerful bright tone he got when he had just found the answer to a case.

That was not the reaction John was hoping for, that was the reaction he was dreaming of but he kept the thought in the back of his mind that Sherlock might be covering something up. Sherlock was a master manipulator.

"Okay, let me go see about a car." Said John getting up, he could risk leaving Sherlock alone for a few minutes in the garden, the staff of the house has long since learned to avoid Sherlock.

John held Sherlock's elbow as they slowly walked up the stairs to 221B Baker Street. Mycroft had arranged for Mrs. Hudson to have her hair done while they were visiting. They felt it would be easier for everyone if they we alone for the visit. He had gained a good deal of weight in the last few weeks but his suits still hung from his body. The ride in the car had been just like normal; John was relieved that would be one less obstacle to overcome in Sherlock's battle for normalcy. Sherlock's ankles were still week so the stairs were always a bit of a challenge. They stepped into the living room, it was like John had never left, and everything was as if they had just gone out for a stroll. Mrs. Hudson must have been keeping the place dusted. John helped Sherlock to his chair, he needed to rest. John sat down across from Sherlock; he never thought he would be back at Baker Street.

"Tea?" asked John.

Sherlock nodded slightly.

Mrs. Hudson had kindly cleaned up the kitchen; John knew that Sherlock would never have left the kitchen so clean. John set about making a cup of tea, just like old times. He had been smart enough to have the cook at house put some in a small container for him just in case. Everything was where it had been before his departure. John was putting the tea bags in the bin when he heard the sound of plucking strings, he smiled. By the time John return to the sitting room Sherlock was quietly playing. John had spent many hours lying in his bunk dreaming of that sound, and to hear it after recent events made the sound ever lovelier. John settled back into his chair to watch Sherlock.

Sherlock was still playing his violin so John took the chance to go up to his old room. It was just as he had left it, except for his desk. On the desk sat a pile of letters, addressed to John in Sherlock's curly hand, sealed but unmailed. He picked them up one by one, there were six, and tucked them in to his coat pocket. He would read them later. On his way back down stairs he stuck his head into Sherlock's room, it was unkept as ever and lying on Sherlock's pillow was John's missing blue pull over. John was not surprised; Sherlock had probably been using it for an experiment. John quickly departed when Sherlock's music stopped.

"You okay, Sherlock?" called John from the stairs.

"Yes, John." Replied Sherlock just loud enough for John to hear but his tone was not convincing.

The violin sat safely in an empty chair, Sherlock was on the sofa curled up in the fetal position. This had not been uncommon but to see it now made John's heart quicken. John moved around to be near Sherlock; John reached down and put one hand on his shoulder.

"Sherlock, I'm right here." Said John calmly.

"What are you thinking?" asked John.

Sherlock did not respond, John thought about the letters he had found.

"Sherlock, I am not going to leave. I should never have left you, I was angry with you and I left that rule my decision, I missed you from the moment I arrived in Afghanistan. I can't tell you how many times I wanted to email you, but I didn't know what to say to you." He paused. "Sherlock, you are my best friend, you mean the world to me."

Sherlock slowly relaxed and his body uncurled, the tension leaving his body.

"Do you want to come back here, the two of us?" asked John.

Sherlock nodded gently.

"Why don't we go back to Mycroft's and talk about, I don't want you to feel uncomfortable and we will have to set some ground rules?" He paused. "And I can't agree until I can leave you for a few hours at time so that I can go to the store."

Exhausted from their trip to Baker Street, Sherlock slept soundly on the bed, while John sat reading. A pile of Sherlock's books and his violin sat on the table. The trip had been fruitful. Then there was a gentle knock on the door.

"Yes," replied John trying on to disturb Sherlock.

The door opened slowly and one of the staff stepped in.

"Mr. Holmes would like to see you." Said the young woman.

"Thank you." Replied John.

John looked at Sherlock who out cold, John figured it was as good as time as any to risk leaving Sherlock on his own. John left his regimental mug sitting on the table for Sherlock to find, knowing that to Sherlock it would mean something very important, it wasn't gone; he had just stepped out of the room.

"John, sorry for pulling you away from Sherlock but I think you need to see this." Said the elder Holmes as John entered the large dark office. "We believe we have found that film footage that Sherlock was shown that lead him to believe you were dead."

John walked closer to the computer on the screen was the image of an armored vehicle, and a couple of officers.

"This was found on a badly damaged hard drive in a very suspicious warehouse fire in north London." Said Mycroft.

The video began to play; John recognized several of the individuals on the film before his own face appeared.

"I remember the day that was filmed but that's not the road we took, and that is definitely not what happened on that trip."

"I know, there is evidence to suggest that the video was professionally edited to appear that way."

"All they had to do was change the number on the vehicle." replied John. "There are hundreds of those vehicles all over the country that could be any number of dozens of incidents."

But this film clearly showed why Sherlock had become convinced that John was dead, Sherlock had probably been forced to watch it hundreds of time and then he had probably replayed a million times in his mind driving him further and further from the person he way.


	11. Chapter 11

Author's Note: I plan to go back and correct my grammar mistakes in previous chapters sometime this weekend. My ipad doesn't have a spell checker on it. If all goes as planned I should have another chapter for you in the next couple of days. I just have to figure out a couple of transitions.

John sat watching Sherlock sleep, it had been an exhausting day for Sherlock, and he was determined to show that he was ready to return to London. He had woken at some early hour and had spent the morning following the staff around making deductions about them. They didn't seem to care but by lunch he was asleep on the sofa in the sitting room, where he had collapsed after following the house keeper around for nearly an hour. John wasn't bothered to move him so he sat down to read the letters than he had found in his room at Baker Street.

_Dear Dr. John H. Watson_

_15__th__ June (dated two days after he walked out of Baker Street.)_

_I'm writing to apologize for what I said to you on the day you left. I am sorry, I didn't mean those things, and you are in fact the most important person in my life._

_Sherlock Holmes_

_Dear John H. Watson _

_19__th__ June_

_I hope you are doing well in Afghanistan, Mycroft has told me that you have returned to front lines. Please come home safe._

_Sherlock Holmes_

_Dear John H. Watson_

_20__th__ June_

_How are you? Baker Street seems so lonely without you. I wish you were here because I would rather like a cup of tea and we are out of milk again._

_Sherlock Holmes_

_Dear John_

_21__st__ June_

_I miss you._

_Sherlock _

_Dear John _

_22__nd__ June_

_Pease keep yourself safe, it is hard enough living without you I can't imagine a life without you at all._

_Sherlock _

_John - I need you to come home, I can't do this anymore. You make me a better person. – Sherlock._

John's eyes were tearing, Sherlock had really missed him and wanted him to come home. He could see it in the handwriting which grew worse as the days passed, probably because he hasn't been sleeping well or eating all that much. A part of John regretted leaving because of what had happened to him, but John also knew that he couldn't spend time seconding guessing himself what he needed to do now was focus on Sherlock's recovery. Sherlock had clearly shown that John was the only one he was letting in to the horrible place that his mind was. John was careful to hide the letter among some of his personal possessions so that Sherlock would not find them lying around, they would probably bring up too many questions.

"You found my letters." Said Sherlock, it was a fact not a question.

John nodded, didn't know how long Sherlock had been awake for. He wasn't surprised, now that the nightmares were rare he no longer

Silence filled the room.

John got up from where he sat, went to his ruck sack and removed a small bundle of paper, he looked at them for a long moment before taking them to Sherlock.

"These are my letter's to you." Said John placing them in Sherlock's hands.

_19__th__ June_

_Dear Sherlock Holmes_

_I have returned to the battlefield, it is nice to be making a difference again. I am sorry about what I said, I didn't mean it. You are my best friend and miss you. I hope to see you when I come home. And don't shoot the wall. _

_Dr. John Watson._

_25__th__ June_

_Dear Sherlock_

_Today was tuff, we had two major incidents. I love what I am doing, but losing them is so hard. My nightmares have returned, I thought they had passed but I guess I am wrong. _

_You would have so much fun here, the other day I spend two hours sitting in the mess trying to make deductions about the new group of men that arrived the day before. I don't know if I got anything right but it was a good way to pass the time as we cannot leave the base and you can only spend so much time being bored. _

_Dr. John Watson_

_6__th__ July _

_Sherlock –_

_These last few days have been unending, it is like the blood just won't stop flowing, I haven't slept in days, there is just too much to do, too many lives on the line. _

_There was a young man, no more than 23 or 24, he was fighting so hard to stay alive but he was losing so much blood. One of the nurses and I did everything we could but each time we fixed one thing something else would happen, after nearly two hours of trying he passed. We all fought so hard but it wasn't enough. Sherlock, I don't know if I can keep doing this._

_Wish I was with you._

_John Watson. _

_12__th__ August_

_Sherlock – I just can't bring myself to mail my letters to you, actually I am not even sure you are still living at Baker Street. Maybe one day I will give this letter to you but for now I just do it for my sanity. Harry doesn't return my correspondence, so I am here alone. They keep telling me that writing letters helps with the loneliness but not for me, it just reminds me that the one person I care about it the one person who I walked out on. You mean more to me that you know, you saved me from spending the rest of my life as a cripple wander the streets trying to make a life for myself. You gave me a reason to pick myself up and keep going. Thank you for that. _

_John Watson_

Now Sherlock was crying, John had given him space to read them alone. John went to him, and pulled him into his strong embrace. Neither said anything, they didn't need too they had spend enough time with each other recently that they could communicate with just a simple look and they just needed silence.


	12. Chapter 12

Author's Note: You got lucky, I managed to tie up some loose ends and was able to post the rest of what I have. From here I am going to need some suggestions on where to take my stories.

The next few days passed without incidence, John spent a good deal of time reading in the garden while Sherlock spent time reading, observing or napping with him. They would go for walks around the garden and each day Sherlock grew stronger which is what he needed to do if he was going to return to Baker Street. The letters had been put away and not spoken of, but the changed the situation significantly. They had each forgiven the other, now was a time for healing. Sherlock's physical wounds had healed but they both had emotional wounds that needed patching back up. They wouldn't talk about but time and being together would hopefully do it.

John sat in the garden reading his book enjoying the beautiful spring weather, Sherlock had disappeared some time ago something about an experiment. John didn't follow, at least not yet, Sherlock would be back soon enough and he needed to start venturing out on his own. John was just happy to see Sherlock doing normal things, at least normal for him. Maybe they would be able to head back to Baker Street in the next few days.

"Help." Yelled John. "Help."

Sherlock was lying unconscious in the bathroom, the walls were covered in a spattering of blood, and there was a growing pool on the floor. Sherlock was bleeding, he had already lost a great deal of blood but by some grace he was still breathing. John did what he could to slow the bleeding, grabbing a towel from the rack and using it, quickly wrapping it around the gaping wound in Sherlock' left arm.

"Sherlock, what have you done?" asked John to himself just one of the house staff stepped into the room.

"Ahhh." She screamed before running from the bathroom.

"Still scaring the staff I see." Replied John. "What am I going to do with you?"

A couple of more staff appeared quickly and helped John to get Sherlock off the bathroom floor and into bed. He held Sherlock's arm while one of the guards went to get the needed supplies. Thankfully one of the guards tended to the housekeeper who had passed out upon the sight of so much blood. John was grateful when a nurse appeared to help him deal with the situation.

It was several hours before Sherlock stirred.

"Sherlock, what the heck were you doing?"Asked John sitting on the edge of the bed. John had already removed Sherlock's bloody clothing.

"An experiment." Replied Sherlock.

"You damn well nearly killed yourself with that little experiment."

"Oh,"

"Oh, is right. You nicked a bloody artery in your arm, you are damn lucky I found you when I did."

"I'm sorry, I'm so sorry." Said Sherlock starting to cry.

John was angry at him and he had every right to be. After a few moments John leaned forward and pulled Sherlock into his embrace.

"Hush."

"I didn't mean to, I just wanted to see how blood flowed on the tile." He said through his sobs.

"I know, I've got you."

Sherlock continued to sob for some time in John's shoulder. Eventually Sherlock calmed down and gently pulled away from John.

"How do you feel?" asked John.

"Tired, hungry." Replied Sherlock.

"I am not surprised you lost rather a lot of blood."

Sherlock started to play with the IV that John had put in.

"Leave it alone, I will take it out when you no longer look like you are going to pass out."

John sat with Sherlock, John felt at peace knowing that he had once again been able to help someone else. He had been able to use his skills and knowledge to help someone he cared about. John figured that Sherlock had indeed been trying to do an experiment when the injury caused a flashback which has caused the knife to slip. There was just something about his injury that didn't indicate that is was suicide. John didn't think Sherlock had it in him to commit suicide, they had each other to worry about, they didn't feel complete without the other.

They had only been back at Baker Street for a little over a week as John sat reading the paper with a cup of tea in hand when Sherlock's phone rang, John didn't even look up he had been praying for this day for nearly a week, Sherlock had been driving him crazy. Boredom had set in days ago, they had tried going for a walk but it exhausted Sherlock just to get to the park and back again. He would eat but only went John really got after him about it.

"Yes."

"Good."

"Thank you."

Sherlock never held in depth conversations on the phone, it was about information and it had to be brief. That was Sherlock.

"We have a case." Said Sherlock heading to the door.

John put down his paper and followed Sherlock, just as he had done so many times. John knew today would be different, this was his first case. John knew that this would be a true test of Sherlock's well being, and it scared John but with Sherlock there was no half way. At least John knew he would go chasing down any criminals today, and if he did, he wouldn't get far before his body gave out on him. John just smiled, knowing that this was at least a step in the right direction.

John sat in the stairwell holding Sherlock where he had so suddenly collapsed. Even with his head buried in John's shoulder Sherlock was shaking. Something had triggered this very dramatic and painful response. One moment Sherlock had been standing over the body of a young man in an apartment making deductions about who he was and what had been done to him when Sherlock has suddenly walked out of the room, knocked down Anderson on the way. John followed him knowing perfectly well that something was wrong, very wrong. Anderson yelled something rude to Sherlock but John didn't hear it he was focused on finding Sherlock. John was only a few feet behind him, Sherlock didn't make it far, he was headed down the stairs of the apartment building when his feet gave out from under him and he went tumbling down seven or eight steps, stopping in a heap on the landing. John was at his side within moments, before John could check if he was injured Sherlock had wrapped his arms around John and was pulling John to him. John had managed to move them such that John was sitting with Sherlock on his lap, in a strong embrace. Thankfully no one said anything as they passed, most just averted their gaze. John was just waiting for Anderson to come by and say something smart but for now he was still in the apartment gathering evidence. John didn't know what to do; he figured that for now he would just sit there until the worst of it passed. Maybe he should call Mycroft and see if he could send around a car to take them home.

"John" called a voice softly and gently.

John looked up, it was Lestrade.

"Do you need anything?" asked the Detective Inspector.

John just shook his head not wanting to disturb Sherlock whose tears were running down John's neck. This was not something he thought he would be doing a million years.

"John, I'm sorry."

"It's not your fault, I feared this would happen." Replied John softly. "It's too soon."

"Do you want me to get you a cab?" asked Lestrade.

John pushed Sherlock off of his shoulder a little bit so that they could make eye contact. It was the only way John knew he was listening these days.

"Do you want to go home?" asked John.

Sherlock nodded.

"Please." Said John to Lestrade.


	13. Chapter 13

Author's Note: Sorry this took so long but it was the end of term and today I finally got a few minutes to myself to get the next part of this story on to paper. I always love to hear what you have to the think about the story, plus it inspires me to write faster.

SHERLOCK SHERLOCK

The events at the crime scene left Sherlock exhausted; John sat reading a book while Sherlock napped on the sofa. Mycroft had called John while in the cab, wanting to know if Sherlock was okay. John told Mycroft that he was taking care of things, Mycroft seemed happy enough with his answer. John was prepared to give Sherlock a sedative if he had not fallen asleep on his own when they reached Baker Street. After reading the same page three times John realized his mind wasn't going to focus on anything until he figured out what had triggered Sherlock's reaction to the crime scene, John knew that they had to find a solution because it would destroy everything Sherlock had left if he couldn't do his job. John had learned many things from Sherlock over the years and he tried to recreate the crime scene in his mind and examine it for what may have triggered Sherlock's extreme reaction. John knew it had something to do with an object or an event related to his torture. With Sherlock sleeping soundly next to him John focused his mind going to his own mind palace to find some much need answers.

SHERLOCK SHERLOCK

"John, Sherlock." Yelled a male voice from the stairs.

John was pulled from his mind place.

"John" called the voice again.

John climbed off the bed and headed to the living room, he found Detective Inspector Lestrade in the kitchen.

"Ah, John." Said the detective. "How is he?"

"Asleep." Replied John going to make a cup of tea. "Tea?"

"Please."

"What can I do for you?" asked John filling the kettle.

"I wanted to apologize for today, it was too soon and too gruesome."

"Greg, its not your fault." Said John. "I asked you to call us if you got a new case, it's my fault. I thought he was ready and I still believe he is in many ways."

Lestrade looked at John oddly, he had to trust John, no one knew Sherlock as well as John. Sherlock had taken John's departure very badly just as John had done when Sherlock had faked his suicide some years before. They were two halves of a whole, the other could not function without the other.

"Something at the crime scene caused him to remember something that he has buried deep in his memories, I am trying to figure out what because he has to remember. He has to remember or he is never going to be the man he once was."

"Will he ever fully recover?" asked the detective.

John poured the boiling water in to the tea pot.

"I don't know but I can't stop trying. He didn't give up on me after his death so I am not going to give up on him."

"I wouldn't expect anything less."

John smiled, of all the people in the world Lestrade knew more of his and Sherlock's relationship than anyone.

"Just give it a couple of days, I will text you when he has had some sleep and eaten something."

"He's still not eating." Said the detective taking the proffered cup of tea.

"Has he ever?" John paused. "I just want to get a few more pounds on him."

Lestrade followed John into the sitting room.

"Happy to be back in London?" asked Greg wanting to give John something to talk about other than Sherlock.

"Anything is better than Afghanistan." Said John. "Although it is nice to not have tip toe around Mycroft's staff."

"Do you want me to stay with him for a few minutes, I don't imagine you get much time to go out these days." Said the detective.

John looked at his watch, he wasn't sure how much longer Sherlock would sleep for and leaving him was risky, he could not predict how Sherlock would react if woke up to find John not there.

"Let me think about it, I don't know how he would react if he awoke and I wasn't here."

"I understand."

Lestrade took the hint and quickly turned the subject to cricket, something that they both enjoyed watching when they had the opportunity. John seemed to be enjoying the chance to do something normal, Greg suspected that John hadn't done that since he had been dragged from the deserts of Afghanistan.

SHERLOCK SHERLOCK

"John" Sherlock called out.

John quickly rose from his chair, putting his mug on the mantle before hurrying down the hall.

"John" called Sherlock again.

"Sherlock," said John pushing open the door.

Sherlock was sitting up in bed, his knees pulled up to his chest, arms wrapped around them. He was rocking back and forth, he was very agitated. John quickly went and sat down next to Sherlock. John's proximity was enough to calm Sherlock slightly.

"You okay?" asked John.

Sherlock just shook his head, unable to put his answer in to words.

"Is it about what happened at the crime scene?"

Sherlock nodded in response.

"You did very well, you solved the case." He paused. "And you knocked out Anderson."

Sherlock responded with a huff. Neither knew what to say, John knew that the issue needed to be addressed but he could see that Sherlock was still exhausted.

"Lestrade's here." Said Sherlock.

"I know, do you mind if he stays with you for a few minutes, I need to run to the store we are out of milk." Said John testing the waters.

"As long as he stays out there." Said Sherlock looking towards the door.

"Will you okay without me?" said John.

Sherlock nodded.

"Try to go back to sleep, we can have dinner when I get back, and if you need anything text me." Said John.

John quietly closed the door on the bedroom and returned to the sitting room.

"Is he okay with me being here with him?" asked Lestrade.

"Yes, text me if anything happens, I am only going to the Tesco's up the street." Said John getting his coat.

John headed to the door, for the first time in nearly three months he was leaving Sherlock, he was looking forward to the few minutes of personal time but scared of what might happen while he was way. He took a deep breath and pulled up the door to leave 221 Baker Street.


	14. Chapter 14

Author's Note: I am sorry this took so long; I have been rather busy doing job interviews and keeping up with doing some extra work to stay on top of the bills. Hopefully this is good with everyone. If you find a mistake or have some suggestions for improving the "fight" scene please share them.

SHERLOCK SHERLOCK

John was at the corner when he stopped for a moment and removed his mobile from his packet to check that it was on and the ringer was loud enough for him to hear it over the city traffic. Part of him was surprised that he had made it as far as the corner without a call from Lestrade. John held on to his phone as he crossed the street. He walked quickly wanting to make the trip as short as possible. John thought about texting Sherlock to check on him but Lestrade was with him so he didn't waste the time, he had yet to learn to text and walk at the same time. When he reached the store he quickly grabbed some milk and some of Sherlock's favorite biscuits. He had brought cash, he did not have the time to deal with the chip and pin machines. He was just accepting his change when his phone rang, he was taken by surprise. He quickly glanced at the text as he exited the store.

_How much longer? -SH_

John hocked the bag over his arm and text back.

_Just leaving the shop. - JW_

John pocketed his phone and began to quickly walk back to Baker Street. He knew in his gut that something was wrong.

_Please hurry. - SH_

John wondered about texting Lestrade to ask him what was going on but that would take time that he could use to keep walking to get home sooner. He was just happy to be out of the flat for a few minutes getting so much needed fresh air and some alone time. Although his thoughts were still only of Sherlock at least he didn't have to worry about him for a few minutes, he was being watched of by Lestrade.

SHERLOCK SHERLOCK

John ran up the stairs to the flat, Lestrade was sitting where John had left him not twenty minutes before. Nothing seemed to out of sorts that didn't mean that everything was okay because with Sherlock nothing was as it seemed.

"Hello," said John looking around the flat.

"That was quick," said Lestrade.

"Is something wrong?" Asked John.

Lestrade shook his head standing up. John put the bag on the kitchen table and headed for Sherlock's room. There were no sounds coming from the room.

"Sherlock," said John knocking on the door.

"John," replied Sherlock in a panicked tone.

John opened the door entering the room; Sherlock was on the floor on the far side of the bed curled up in a ball.

"Sherlock, what's wrong?" Said John walking around the bed.

"I need to use the loo." Said Sherlock.

John had to suppress a smile. To an outsider it would appear funny that Sherlock was too scared to leave the room to go the two paces to the bathroom down the hall but John knew better, for Sherlock it would have been a leap of faith that he was not ready to take. Sherlock wouldn't leave the flat without John; he wouldn't even visit Mrs. Hudson. Leaving him with Lestrade had been a huge step.

John put out his hands and helped Sherlock to his feet, together they walked to the bathroom. John stood outside while Sherlock took care of his needs. When he was done Sherlock went back to his room, John watched him go.

"I will call you when dinner is ready," said John heading back to the sitting,

Lestrade was on the phone pacing the small sitting room, John could tell that it was worked related so he went to turn on the kettle and set about making dinner.

"Everything okay?" Asked Lestrade.

"Yes," replied John, he wouldn't say anything about Sherlock not wanting to leave his room to use the loo.

"Sherlock was correct, it was the partner, he admitted it all." Said Lestrade after looking at text on his phone.

John smiled, Sherlock had solved another one, his first since his ordeal, and hopefully it wouldn't be his last.

"He drowned him in the bath in a jealous rage." Added the detective.

That's when it all made sense to John, it was the water, it was the fact that the man had been drowned. John knew that Sherlock had been subject to some sort of water torture but did not on know the details. What he did know was the Sherlock would not take a shower and that when he did bath John had to be there no matter what. John would still help him with some things but mostly he just sat and read the paper, Sherlock would panic if he even tried to leave the room.

Silence filled the space while John set about making dinner for himself and Sherlock.

"Do you want to stay for dinner?" asked John.

"I had better not; I don't want to make any more upset than he already is."

"Don't worry about him; it's nothing you did really."

"But I do worry, even after everything I have seen he has never been like this." Said Lestrade.

"Give it time; we have only been back here at Baker Street a fortnight."

Greg started towards the door.

"You take care of him and I will see about finding you some more cases."

"Thanks." Replied John. "And thanks for watching him so I could run to the shop."

"Call me if you need anything." Replied Greg heading down the stairs.

John listened as the door leading out was opened and then firmly shut and quickly followed by Sherlock coming out of his room.

"Is he gone?" asked Sherlock timidly.

"Yes," John held is tongue at that.

"Good." Said Sherlock heading for the sofa.

SHERLOCK SHERLOCK

After dinner John settled in to watch some mindless show, Sherlock had eaten half a bowl of pasta before taking up residence on the sofa. He seemed happier now that they were once again alone in the flat. Mrs. Hudson had long since given up visiting outside of her normal Tuesday morning visit with John, Sherlock never reacted well to her unexpected visits. John wasn't really watching the telly, his mind instead drifted back to the night much like this one when everything had changed.

_John slowly climbed the stairs up to the flat, it had been a very rough day at the clinic. He had given a lovely old woman the horrible news that she probably wouldn't make it to Christmas, she had cancer. Then there was the young man who was looking to marry who now had to deal with the news of having HIV. It had been a very rough shift and it was made worse knowing that he was going home to a very bored Sherlock Holmes. He hadn't had a case in over a week and it was growing tedious. All John wanted as a strong cup of tea and a few minutes to reflect on his day without interruption. _

_When john entered the flat Sherlock was laid out on the sofa dressed in his suit pants, a dress shirt and his blue silk dressing gown, it was were John had left his that morning. John headed into the kitchen, he put the kettle on, pulled out two mugs, dropped in a couple of tea bags and went to the fridge to get the milk. He opened the door just waiting for today's surprise, today it was a hand._

"_Where's the milk?" asked John._

"_I needed the bottle for an experiment." Replied Sherlock, his voice muffled by the sofa. _

"_I only picked that up yesterday when you left the last bottle out to go off." Said John taking a couple of deep breaths. _

"_Bad day at the clinic?" asked Sherlock._

"_Yes, nice observation, it was a bloody brilliant day at the clinic." Replied John_

"_John, it doesn't matter." Replied Sherlock rather off handedly._

"_Of course it matters, three people will not get to do fulfill their dreams."_

"_They don't matter."_

"_Then what really matters, Sherlock?"_

"_The work." He replied. "They are just idiotic drones wandering through life on some meaningless journey through life."_

"_Thank you Sherlock, thank you for making that so clear to me."_

_John put on his coat, he needed out the apartment before he lost his temper, he didn't have the energy to fight with Sherlock, not after today._

"_Where are you going?" asked Sherlock._

"_I need some fresh air," said John._

"_Just open the window." Said Sherlock still not moving from his place on the sofa._

"_You are an idiot, I need out of the place, I need away from you. I just wanted to come home and have a cup tea but no you decided to toss my milk so that you could use the bottle for one of your experiments. You don't think of anyone other than yourself, like last week when you left me in some mysterious part of London without cab fair or when you destroyed one of my good sweaters a few weeks back." He paused. " When I can't keep up with you, you call me an idiot or worse, then you remind me just how useless I am and then you expect me to ignore the simple fact that you make me feel like I am worthless to you. I can't do this anymore, you just take, take, take and give nothing in return except rude comments and hurt feelings."_

_John walked out of the kitchen and up to his room, he pulled out his ruck sack and suitcase from the closet. And hour later he was out of the door and in a cab to his sister's. _

There was still so much that needed to be said but it would never happen, Sherlock might have changed in many way but there were some things that would never change.

"John." Said Sherlock.

"Yes," replied John.

"I am sorry I made you leave." Said Sherlock.

"It doesn't matter now Sherlock, I am here now."

"It does matter," said Sherlock. "When you left . . . . "

John got up from where he sat and moved to the sofa, he kneeled down next to the sofa. John placed his hand on Sherlock's shoulder; John hadn't noticed how tense Sherlock was when he started to relax at John's touch.

"I am here now."

Sherlock rolled to face John, something wasn't right. John pulled Sherlock into an embrace. Sherlock began to sob gently; John slowly rubbed circles on Sherlock's back to calm him. Something had upset him, probably the incident at the crime scene. Since John's return Sherlock no longer fled from human contact at least with John.

"Was it the water?" asked John eventually.

Sherlock nodded gently still tucked up against John's chest.

That confirmed John's suspicion, John would put money on that at some point Sherlock had been subject to some level of torture that may have led to being drowned.


	15. Chapter 15

Author's Note: Well, I went back and added a few lines to the last chapter hopefully to make some more impact on the falling out between John and Sherlock. I will probably only have one or two more chapters before I wrap this one up. Thank you for everyone's support and keep the reviews coming, they make me write faster.

SHERLOCK SHERLOCK

"Do you want to tell me what happened?" Asked John.

Sherlock continued to tremble in John's embrace. It was some time before Sherlock made any attempt to separate himself from John, when he did John managed to sit himself down on the sofa so he was sitting next to Sherlock.

"It might help if you told me what happened." Said John, he wasn't going to push the matter, now it was Sherlock's turn. John could see Sherlock thinking, it was a tell that he had learned not long after moving in with Sherlock, there was just something about the look that would develop on his face when he was in his mind palace.

"He would cover my face with a dirty rag," said Sherlock hardly above a whisper his voice shaking just as his hands did.

John took Sherlock's trembling hands trying to comfort Sherlock.

"Heavy cotton, it smelled of motor oil, blood, urine and feces, probably my own."

Only Sherlock would remember so much detail of his torture, even under stress he noticed the little things. It was the curse of his gift, even when he didn't need to remember the small stuff he would.

"He would spray me with cold water." Continued Sherlock, his voice still unsteady.

"He would do it until I passed out, I was so scarred I would never wake up, that it would be the last time." Sherlock's whole body trembled.

John put an arm around his friend.

"What did he want?" asked John scared it might be too much.

"He wanted to break me," said Sherlock softly as if he didn't want anyone to know other than John. "He wanted to destroy me and he did."

"He didn't destroy you." Said John trying to be supportive at this critical juncture.

"But I can't work.""

"Sherlock, today was just a bump in the road. You solved the case." John was unsure of what to say to his friend. "We will get through this, you and I can do this together, you are not alone, I am here and I am going to stay here."

Sherlock started to show tears but was taking long deep breaths to control his emotions.

"Tell me." Said John.

"I was scared I would never see you again John." Sherlock voice remained quiet but grew more steady as he spoke. "I kept telling myself that if I made it out alive I would do anything to find you."

John was happy to have Sherlock finally open up to him about his ordeal, he was amazed to discovered that he had been Sherlock's anchor through it.

John looked at the clock, it was getting late.

"Let's get you to bed, it has been a rough day," said John standing up.

Sherlock said nothing, he only reached out for John's hand to help him stand up from where he sat. John pulled Sherlock to his feet and they walked together to Sherlock's room. John settled Sherlock in to his bed, making sure there was nothing to constrict his movements. Several time in the last fortnight Sherlock would awake tangled in his bedding screaming. There was little that could be done.

"Stay" said Sherlock quietly as John headed for the door.

John almost missed his friend's plea, but it wasn't unexpected.

"Let me just go get ready for bed." Said John.

Sherlock relaxed slightly.

SHERLOCK SHERLOCK

Sherlock was still asleep when John got up, he had spent the night on his bedroll on the floor next to his friend. The floor was not conducive to a good night's sleep or to the health of his shoulder. His shoulder was a sore from the hard floor but it was a small price to pay for knowing that Sherlock had slept through the night. John headed to the shower hoping the hot water would calm the growing pain in his shoulder. Sherlock was still sleeping soundly, he had kicked off the duvet, it not lay in a pile on the floor on the far side of the bed.

John was just about to get out of the shower when he discovered Sherlock standing in the bathroom watching him.

"Sherlock." Said John startled at the sight.

Sherlock was wearing only a pair of shorts, he was trembling slightly.

"Shit, I'm sorry." Said John thinking that Sherlock had been frightened when he wasn't there with him when he had awoken.

Sherlock took a step forward, John went to reach to turn off the water but he was stopped. Sherlock grabbed his hand.

"Help me." Said Sherlock.

John stepped to one side, Sherlock shed his shorts and got into the shower with John. John was uncomfortable but then Sherlock's idea of personal space and privacy was nonexistent between them. When the water first started to hit Sherlock's skin he started to tremble, he took several long deep breaths trying to control his reaction.

"You don't have to do this." Said John.

"Yes I do." Said Sherlock stepping under the running water.

John could see that Sherlock's body was starting to betray him so instinctually he went to Sherlock and pulled him into his embrace. Together they stood under the running water, Sherlock's trembling form slowly relaxing. When the water started to run cold John immediately shut off the water. He released Sherlock, only to grab a towel from the warming cupboard and wrap is around Sherlock's thin form, before dealing with himself.

SHERLOCK SHERLOCK

John was making tea when Sherlock appeared from his bedroom fully dressed. He came to stand in the entrance to the kitchen.

"How are you?" asked John.

"Thank you." Said Sherlock softly.

John had to suppress the smile that he felt growing in him, he was very proud of what Sherlock had done.

"We will get through this and you will file, just give it time." Said John handing Sherlock a cup of tea on his way to the living room to read the morning paper.

"Why did you come back?" asked Sherlock.

"I wasn't given much choice." Said John lightly. "Your brother called in a favor and had me shipped home."

"When I left Afghanistan I did not know any details only that you were in trouble, I wouldn't have admitted it then but I wanted to see you." John paused taking a sip of tea. "Mycroft was waiting for me when I arrived he gave me some brief details in the car on our way to the estate."

"When I saw you in that room, my heart broke, and I knew that I had to do everything in my power to help you."

There was an awkward silence in the flat, both men sipping at cups of tea.

"Thank you." Said Sherlock.

"As I said at grave stone all those years ago, I was so alone, if I hadn't met you I can imagine what my life would be like. I couldn't leave you to suffer the same loneliness that I felt after being shot."

"I am sorry I pushed you away, I said some very hash things to you that I didn't mean. You are not an idiot, and I need you in my life. You are my only friend."

"I know that, Sherlock." Said John gently.

Sherlock looked a bit nervous.

"After you left, I did something I am not very proud of."

"The morphine?" asked John.

Sherlock nodded.

"Sherlock you don't have to say anything, we both acted like idiots, that is the past." John paused. "I am here to stay so let's try working on today."

"You did really well this morning," said John taking his now empty mug into the kitchen. "Do you want to go out for a walk later?"

"Maybe if we don't get a case." Said Sherlock.


End file.
